genotan -m <microsatellite list file> <sam or bam file> [-o <output file>] [-L off] [-C <0.01-0.99>] [-c <0.01-0.99>] [-q <0-255 >]
-L off : Turn off the normalization of read counts using the allele lengths (default : on)
-C FLOAT [0.01-0.99] : If a confidence score of a higher read frequency allele at a locus is lower than the cutoff value, a genotype of the locus will not be reported. (default : 0.35)
-c FLOAT [0.01-0.99] : If a confidence score of a lower read frequency allele at a locus is lower than the cutoff value, the allele will not be reported. (default : 0.25)
-q INT [0-255] : if a mapping quality of a read is lower than the cutoff value, the read will not be used. (default : 5)
-O INT [0: no sequence, 1: sequence output]: It decides the output style. (default : 1)